You can do this in Encore.
I am assuming you are only picking presets, and not customizing one. You pick prests in the Transcode Settings dialog. Do you see the "Edit Quality Presets" button? Pick it, customize one by setting the bitrates to get the results you want, then SAVE IT as your own. Then pick that in the transcode setting. (In the transcode setting image, you can see my custom example "Stan Custom 4Mb CBR".) And yes, you can select all your video assets and apply this custom preset to all of them at once. I would do one short one to see if you are getting in the ball park. I would do 2 samples: one in MPEG2-Bluray and one in H.264-Blu-ray. (I'd follow Richard's recommendation to you and use H.264.)
